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Yorodumi- PDB-1hsa: THE THREE-DIMENSIONAL STRUCTURE OF HLA-B27 AT 2.1 ANGSTROMS RESOL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hsa | ||||||
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Title | THE THREE-DIMENSIONAL STRUCTURE OF HLA-B27 AT 2.1 ANGSTROMS RESOLUTION SUGGESTS A GENERAL MECHANISM FOR TIGHT PEPTIDE BINDING TO MHC | ||||||
Components |
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Keywords | HISTOCOMPATIBILITY ANTIGEN | ||||||
Function / homology | Function and homology information regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / secretory granule membrane ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / defense response / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1992 Title: The three-dimensional structure of HLA-B27 at 2.1 A resolution suggests a general mechanism for tight peptide binding to MHC. Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C. #1: Journal: Nature / Year: 1991 Title: The Structure of Hla-B27 Reveals Nonamer Self-Peptides Bound in an Extended Conformation Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C. #2: Journal: Nature / Year: 1991 Title: Identification of Self Peptides Bound to Purified Hla-B27 Authors: Jardetzky, T.S. / Lane, W.S. / Robinson, R.A. / Madden, D.R. / Wiley, D.C. #3: Journal: Proteins / Year: 1992 Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Human Major Histocompatibility Antigen Hla-B27 Authors: Gorga, J.C. / Madden, D.R. / Prendergast, J.K. / Wiley, D.C. / Strominger, J.L. #4: Journal: J.Mol.Biol. / Year: 1991 Title: Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution Authors: Saper, M.A. / Bjorkman, P.J. / Wiley, D.C. #5: Journal: Nature / Year: 1989 Title: Specificity Pockets for the Side Chains of Peptide Antigens in Hla-Aw68 Authors: Garrett, T.P.J. / Saper, M.A. / Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C. #6: Journal: Nature / Year: 1987 Title: Structure of the Human Class I Histocompatibility Antigen, Hla-A2 Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C. #7: Journal: Nature / Year: 1987 Title: The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens Authors: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C. #8: Journal: J.Mol.Biol. / Year: 1985 Title: Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes Authors: Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C. | ||||||
History |
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Remark 700 | SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE ...SHEET SHEETS 2 AND 4 EACH HAVE ONE STRAND THAT IS BIFURCATED. THIS IS REPRESENTED BY PRESENTING THE SHEETS TWICE (DESIGNATED SHEETS SB1, SB2 AND SD1, SD2 RESPECTIVELY) WHERE THE TWO REPRESENTATIONS DIFFER IN THEIR LAST STRAND. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hsa.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hsa.ent.gz | 139.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/1hsa ftp://data.pdbj.org/pub/pdb/validation_reports/hs/1hsa | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO A 210, PRO B 32, PRO D 210 AND PRO E 32 ARE CIS PROLINES. 2: SIDE CHAIN ATOMS OF ARG A 108, LYS A 268, LYS B 58 AND ARG D 108, LYS D 268, LYS E 58 ARE DISORDERED, AND HAVE OCCUPANCIES EQUAL TO ZERO IN THIS ENTRY. 3: THESE SOLVENT MOLECULES ARE LOCATED WITHIN THE PEPTIDE-BINDING SITE OF COMPLEX 1. 4: THESE SOLVENT MOLECULES ARE LOCATED WITHIN THE PEPTIDE-BINDING SITE OF COMPLEX 2. |
-Components
#1: Protein | Mass: 31928.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P03989, UniProt: P01889*PLUS #2: Protein | Mass: 11748.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P61769 #3: Protein/peptide | Mass: 743.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | Compound details | SECONDARY STRUCTURE SPECIFICATIONS WERE MADE BY USE OF THE PROCEDURE OF W. KABSCH AND C. SANDER ...SECONDARY STRUCTURE SPECIFICAT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.54 % | ||||||||||||||||||||||||||||||
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Crystal grow | Details: THE FRAGMENT CRYSTALLIZED WAS THE EXTRACELLULAR PORTION OF THE PROTEIN CLEAVED FROM DETERGENT MICELLES WITH PAPAIN | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 8.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 10 Å / % possible obs: 92 % / Rmerge(I) obs: 0.077 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.203 / Rfactor obs: 0.203 / Highest resolution: 2.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.1 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 5.5 Å / Rfactor obs: 0.203 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.203 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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